A "pay-per-use" stock picture of the desired structure is only semi-relevant to your question.
Head over to Bristol university's molecule of the month collection at
www.chm.bris.ac.uk/motm/motm.htm, find the Methamphetamine entry in the table and select its "vrml" version
(the "V" behind the name).
Among the text, you will find a few illustrations of the molecule - click on them to download the 3d version.
This file format should be printable on shapeways, even in color.

Did you check the link in my message ? While the chemical formula on that page is a conventional line drawing, the VRML (extension .wrl)
file it links to is the color-coded 3D ball-and-stick model you want, and should be directly uploadable to shapeways.

I see that JACANT beat me to it, thanks.
Regarding ChemDraw - probably yes, if it can export true 3D coordinates in the PDB format originally created
for the Protein Data Bank ("true" 3D coordinates in the sense that they contain more than just the flat drawing
with z=0 - I do not know ChemDraw's capabilities). The import options of meshlab for pdb appear to be quite limited,
apparently it will create a "space-filling" model, but not a ball-and-stick one. The freeware RasMol program, however,
should allow you to generate the kind of VRML file you want from a PDB one.
Another alternative might be to try to find data from a crystal structure determination, e.g. in the "Crystallography Open
Database" and work from there.

Filters -> Normals, Curvatures and Orientation -> Transform:Scale
Set "XAxis" to 0.5, make sure that "Uniform Scaling" is checked, check
the "Preview" box if you like, then click on "Apply" if you are satisfied with
the settings.

Oh well... VRML export from meshlab appears to be broken. And that wrl file is overly
complex anyway - one extremely detailed mesh that just represents a tiny blue sphere
that once must have been the anchor point for switching between the several viewer
positions in the file. (And the molecule itself is a single mesh, not a collection of vrml
"sphere" and "cylinder" primitives that would facilitate changing individual radii...)
Try this one here instead http://shpws.me/k9gC - i have removed
the unnecessary viewpoints and the selector sphere, and added a scaling transformation
at the top. Just open it in a text editor, find the line that reads "scale 0.5 0.5 0.5" and change
it if necessary. (With this scale, an upload specifying "Inch" as the base unit results in a
model that is 5 by 2.1 by 1.8 in and would cost something like $15 in "full-color sandstone"
or $20 in paint-it-yourself WSF plastic.

Please see updated file, half size. http://www.shapeways.com/model/728611/
As mkroeker pointed out there is a small isolated sphere approx .7mm. You can just see it in the center of the image. I don't think this will affect the print. Surely it will just get lost in the printing process. You could ask service@shapeways.com